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Final Exam Study Guide This study guide is not exhaustive; anything from the course is fair game for the cumulative final exam. Note that main ideas are included and you need to go back to your notes, outlines, and worksheets to make sure you are familiar with the topics. Chapter 1 Characteristics of living things Hierarchical organization of living systems Cell theory Molecular basis of heredity Relationship between structure and function Evolution gives rise to diversity Living systems use energy to exist in non-equilibrium states Chapter 2 Matter Element Atoms Protons Neutrons Electrons Energy levels in atoms Cations Anions Redox reactions Oxidation Reduction Valence electrons Octet rule Chemical Bonds Ionic bonds Non-Polar covalent bonds Polar covalent bonds Hydrogen bonds Chemical reactions alter bonds! Properties of water Chapter 3 Chemistry of carbon 6 elements make up macromolecules Monomers Polymers Macromolecule Dehydration synthesis Hydrolysis 4 Groups of Macromolecules, structure, function, and examples Carbohydrates Nucleic Acids Proteins Lipids Chapter 4 Cell Theory: Cell size Basic Requirements to be a cell Prokaryotic Cells vs. Eukaryotic Cells Examples of organisms Characteristics of cells Structures of cells Eukaryotic cell Nucleus Ribosomes Rough ER Smooth ER Golgi apparatus Lysosomes Peroxisomes Vacuole Mitochondria Chloroplast Endosymbiant Theory Cytoskeleton Extracellular Structures and Cell Movement Cell-To-Cell Interactions Adhesive junctions Tight junctions Gap (communication) junctions Chapter 5 Structure of Membranes phospholipids proteins cell surface markers Passive Transport Concentration gradient Diffusion Facilitated diffusion Osmosis Isotonic Hypertonic Hypotonic Active Transport Endocytosis Exocytosis Chapter 6 Flow of Energy in Living Systems Potential energy Kinetic energy Chemical energy Redox reactions Laws of Thermodynamics and Free Energy Endergonic reactions Exergonic reactions Activation energy and graphs ATP – adenosine triphosphate Enzymes Induced fit model. Enzymes affected by: Temperature pH Inhibitors and activators Metabolism – sum of all chemical reactions Anabolic Catabolic Chapter 7 Cellular Respiration Autotrophs Heterotrophs Aerobic Anaerobic Fermentation ATP Prooduction Substrate level phosphorylation Oxidative phosphorylation For each major phase of Cellular Respiration, you should know where it takes place, the reactants, products, and biproducts. Glycolysis Oxidation of Pyruvate to Produce Acetyl-CoA Kreb’s Cycle Electron Transport Chain and Chemiosmosis TOTAL NET YIELD FROM AEROBIC RESPIRATION: Glycolysis 2ATP Krebs 2 ATP ETC 34 ATP 36-38 ATP Anaerobic cellular respiration Fermentation Chapter 8 Anoxygenic photosynthesis Oxygenic photosynthesis THE KIND OF PHOTOSYNTHESIS DESCRIBED IS FOR C3 PLANTS; EXCEPTIONS WILL BE NOTED AT THE END OF THE CHAPTER Photosynthesis has 3 distinct phases Capture of light energy Production of energy (ATP and NADPH) Synthesis of organic molecules 6CO2 + 12H2O + light C6H12O6 + 6 H2O + 6O2 chloroplast Thylkoid Stroma Cholorphyll Light dependent reactions (LDR) Photosystems II, ETC, and PS I roles and end products Light independent reactions (LIR) Calvin cycle, 3 phases, where it occurs, reactants and products, enzyme Photorespiration C3, C4, CAM Chapter 10 Bacterial Cell Division Eukaryotic chromosomes Humans have 46 chromosomes (23 homologous pairs) DNA Condensed structure Haploid Diploid Homologous pairs Cell Cycle; know the phases of I and M, and what happens in each Interphase Mitosis Cytokinesis 3 major checkpoints: G1/S primary checkpoint G2/M Spindle Cancer Proto-oncogenes Tumor suppressor genes Chapter 11 Sexual Reproduction Requires Meiosis Meiosis occurs in gametes Meiosis functions in the production of sex cells 4 genetically different haploid cells are produced Know what goes on in phases of Meiosis, especially what makes it different from mitosis Meiosis versus Mitosis Chapter 12 Heredity True-breeding Hybrids Gregor Mendel Monohybrid cross Principle of segregation Pedigrees of dominant traits Pedigrees of recessive traits Di-hybrid crosses Principle of independent Testcross Polygenic inheritance Pleiotropy Multiple alleles in a human population Incomplete dominance Co-dominance Epistasis Environmental effect on phenotype Chapter 13 Chromosomal Theory of Inheritance Sex Chromosomes and Sex Determination Autosomes are homologous Sex chromosomes are not Female carries XX Male carries XY Sex Linkage; males and inheritance of sex linked recessive traits Dosage compensation In females one X chromosome is randomly selected for modification Genetic Mapping Frequency of recombination is related to relative gene loci. Nondisjunction leads to aneuploidy Monosomics Trisomics Nondisjunction of sex chromosomes Chapter 14 Chromosomes are composed of DNA and protein: DNA carries genetic info DNA Structure 3 components of a nucleotide Purines & Pyrimidines Chargaff’s Rule Rosalind Franklin Watson and Crick’s Double helix: bonds between nucleotides vs nitrogen-bases 2 Anti-parallel strands one 5’3’ and the other 3’5’ Semi-conservative Model of DNA replication Prokaryotic Replication: Single circular chromosome Begins at A=T rich region (A=T only have 2 H-bonds) and proceeds bi-directionally Know enzymes for DNA replication and their functions: Helicase SS binding proteins DNA gyrase Primase DNA polymerase III( adds nucleotide in 5’ to 3’ direction) DNA polymerase I Ligase Leading strand vs. Lagging strand Synthesis Okazaki fragments Eukaryotic Replication: Multiple linear chromosomes & Multiple origins of replication Telomeres are replicated using telomerase DNA Repair: DNA polymerase II Chapter 15 One gene / one polypeptide hypothesis. The central dogma of molecular biology DNA –transcription RNA –translation proteins Modified with discovery of reverse transcriptase (found in retroviruses) DNA ↔ RNA proteins RNA’s and their functions: mRNA, tRNA, rRNA, snRNA, SRP RNA, MicroRNA Genetic Code: 64 codons & is degenerate Stop codons: UAG, UAA, UGA Start codon: AUG, (methionine) in prokaryotes codes for a slightly different methionine Wobble effect at third position For both Prokaryotes and Eukaryotes know initiation, elongation, and termination for transcription and translation Prokaryotic Transcription Initiation: Promoter – sequence within DNA Elongation uses RNA polymerase to add ribonucleotides that are complementary to the template strand of transcription unit Most common mechanism for termination is the formation of a hairpin structure In prokaryotes transcription and translation happen simultaneously. Eukaryotic Transcription Initiation: Promoter (differs for different polymerases) -10 sequence and TATA box Elongation occurs in the same fashion, but eukaryotes have multiple RNA polymerases Termination sites not well defined Posttranscriptional mRNA processing 5’ cap allows for ribosome to bind 3’ poly A tail to protect the mRNA Introns—interveneing sequence/ non-coding Exons—expressed sequence only 1-1.5% of genome Alternate splicing allows one transcript to code for multiple proteins Process of Translation Initiation Initiation factors associate Initiator tRNA enters ribosome Small subunit of ribosome binds mRNA Large subunit of ribosome binds small subunit Elongation tRNA with anticodon that can bind codon enters A site peptide bond formed in P site empty tRNA leaves ribosome translocation repeat Termination Stop codon is reached Release factors enter ribosome and release, ribosome subunits and mRNA Direction to roughER via SRP RNA Mutations: Altered Genes Point mutation – insertion, deletion, substitution Chromosomal mutations: Deletions, Duplication, Inversions, Translocation Chapter 16 Prokaryotes regulate gene expression in response to their environment Eukaryotes regulate gene expression for development and maintenance of homeostasis Use transcription factors to initiate transcription Posttransciptional Regulation Alternate splicing and mRNA editing mRNA longevity Transport out of the nucleus Initiation of translation Small RNAs and microRNAs cause RNA interferencce Table 16.19 Controlled turnover of non-functional proteins Chapter 17 Recombinant DNA—genetic information from two species Restriction endonucleases (restriction enzymes) Gel electrophoresis uses an electric current to separate DNA based on size. (-) charge of DNA is attracted to the positive charge of the electric current. PCR makes millions of copies of a sample of DNA Then the DNA of interest can be sequenced to determine the order of nucleotides DNA libraries contain entire genome of an organism contained in vectors cDNA libraries contain the coding genome of an organism Reverse transcriptase is used to make cDNA cDNA (coding DNA) only includes exons for a certain polypeptide. Southern blot detects DNA Northern blot detects RNA Western blot detects proteins DNA fingerprinting uses restriction enzymes and gel electrophoresis Chapter 18 Genetic maps show the location of genes on chromosomes DNA Sequencing is the ultimate physical map is entire genomic sequence Human Genome Project 25,000 genes in human genome Protein coding genes have start codon, open reading frame, then stop codon. Types of Noncoding DNA in eukaryotes (makes up 99% of human DNA) mRNA can be isolated and used to make cDNA Only 25,000 genes, but 87,000 cDNAs (which code for proteins) made from human cells!!! Alternative splicing Functional genomics Proteomics Transcriptomics Chapter 19 Stem cells – capable of both continual division and differentiation Totipotent Pluripotent Multipotent Unipotent Somatic cell nuclear transfer (Dolly) Egg is enucleated, DNA from somatic cell added to egg, stimulate for cell division, implant in surrogate mother. Problems with this approach seem to stem from our inability to successfully rewind molecular clocks, “the DNA of somatic cell is old”